                      :-) GROMACS - gmx mdrun, 2021.5 (-:

                            GROMACS is written by:
     Andrey Alekseenko              Emile Apol              Rossen Apostolov     
         Paul Bauer           Herman J.C. Berendsen           Par Bjelkmar       
       Christian Blau           Viacheslav Bolnykh             Kevin Boyd        
     Aldert van Buuren           Rudi van Drunen             Anton Feenstra      
    Gilles Gouaillardet             Alan Gray               Gerrit Groenhof      
       Anca Hamuraru            Vincent Hindriksen          M. Eric Irrgang      
      Aleksei Iupinov           Christoph Junghans             Joe Jordan        
    Dimitrios Karkoulis            Peter Kasson                Jiri Kraus        
      Carsten Kutzner              Per Larsson              Justin A. Lemkul     
       Viveca Lindahl            Magnus Lundborg             Erik Marklund       
        Pascal Merz             Pieter Meulenhoff            Teemu Murtola       
        Szilard Pall               Sander Pronk              Roland Schulz       
       Michael Shirts            Alexey Shvetsov             Alfons Sijbers      
       Peter Tieleman              Jon Vincent              Teemu Virolainen     
     Christian Wennberg            Maarten Wolf              Artem Zhmurov       
                           and the project leaders:
        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel

Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.

GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.

GROMACS:      gmx mdrun, version 2021.5
Executable:   /usr/bin/gmx
Data prefix:  /usr
Working dir:  /media/romi/Zeus - 1 TB/incomplete-simulation-dataverse/3opz-312k
Process ID:   55473
Command line:
  gmx mdrun -deffnm md_1_20 -cpi md_0_10.cpt -noappend -v

GROMACS version:    2021.5
Precision:          mixed
Memory model:       64 bit
MPI library:        thread_mpi
OpenMP support:     enabled (GMX_OPENMP_MAX_THREADS = 64)
GPU support:        disabled
SIMD instructions:  AVX2_256
FFT library:        fftw-3.3.8-sse2-avx-avx2-avx2_128
RDTSCP usage:       enabled
TNG support:        enabled
Hwloc support:      disabled
Tracing support:    disabled
C compiler:         /usr/bin/cc GNU 9.4.0
C compiler flags:   -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -O3 -DNDEBUG
C++ compiler:       /usr/bin/c++ GNU 9.4.0
C++ compiler flags: -mavx2 -mfma -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops SHELL:-fopenmp -O3 -DNDEBUG


Running on 1 node with total 20 cores, 20 logical cores
Hardware detected:
  CPU info:
    Vendor: Intel
    Brand:  12th Gen Intel(R) Core(TM) i7-12700K
    Family: 6   Model: 151   Stepping: 2
    Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sha sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
  Hardware topology: Only logical processor count


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.
Lindahl
GROMACS: High performance molecular simulations through multi-level
parallelism from laptops to supercomputers
SoftwareX 1 (2015) pp. 19-25
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with
GROMACS
In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
GROMACS 4.5: a high-throughput and highly parallel open source molecular
simulation toolkit
Bioinformatics 29 (2013) pp. 845-54
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
J. Chem. Theory Comput. 4 (2008) pp. 435-447
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
Berendsen
GROMACS: Fast, Flexible and Free
J. Comp. Chem. 26 (2005) pp. 1701-1719
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
E. Lindahl and B. Hess and D. van der Spoel
GROMACS 3.0: A package for molecular simulation and trajectory analysis
J. Mol. Mod. 7 (2001) pp. 306-317
-------- -------- --- Thank You --- -------- --------


++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
H. J. C. Berendsen, D. van der Spoel and R. van Drunen
GROMACS: A message-passing parallel molecular dynamics implementation
Comp. Phys. Comm. 91 (1995) pp. 43-56
-------- -------- --- Thank You --- -------- --------


++++ PLEASE CITE THE DOI FOR THIS VERSION OF GROMACS ++++
https://doi.org/10.5281/zenodo.5850051
-------- -------- --- Thank You --- -------- --------

Input Parameters:
   integrator                     = md
   tinit                          = 0
   dt                             = 0.002
   nsteps                         = 50050000
   init-step                      = 0
   simulation-part                = 1
   mts                            = false
   comm-mode                      = Linear
   nstcomm                        = 100
   bd-fric                        = 0
   ld-seed                        = -1424007207
   emtol                          = 10
   emstep                         = 0.01
   niter                          = 20
   fcstep                         = 0
   nstcgsteep                     = 1000
   nbfgscorr                      = 10
   rtpi                           = 0.05
   nstxout                        = 0
   nstvout                        = 0
   nstfout                        = 0
   nstlog                         = 5000
   nstcalcenergy                  = 100
   nstenergy                      = 5000
   nstxout-compressed             = 5000
   compressed-x-precision         = 1000
   cutoff-scheme                  = Verlet
   nstlist                        = 10
   pbc                            = xyz
   periodic-molecules             = false
   verlet-buffer-tolerance        = 0.005
   rlist                          = 1
   coulombtype                    = PME
   coulomb-modifier               = Potential-shift
   rcoulomb-switch                = 0
   rcoulomb                       = 1
   epsilon-r                      = 1
   epsilon-rf                     = inf
   vdw-type                       = Cut-off
   vdw-modifier                   = Potential-shift
   rvdw-switch                    = 0
   rvdw                           = 1
   DispCorr                       = EnerPres
   table-extension                = 1
   fourierspacing                 = 0.16
   fourier-nx                     = 104
   fourier-ny                     = 104
   fourier-nz                     = 104
   pme-order                      = 4
   ewald-rtol                     = 1e-05
   ewald-rtol-lj                  = 0.001
   lj-pme-comb-rule               = Geometric
   ewald-geometry                 = 0
   epsilon-surface                = 0
   tcoupl                         = V-rescale
   nsttcouple                     = 10
   nh-chain-length                = 0
   print-nose-hoover-chain-variables = false
   pcoupl                         = Parrinello-Rahman
   pcoupltype                     = Isotropic
   nstpcouple                     = 10
   tau-p                          = 2
   compressibility (3x3):
      compressibility[    0]={ 4.50000e-05,  0.00000e+00,  0.00000e+00}
      compressibility[    1]={ 0.00000e+00,  4.50000e-05,  0.00000e+00}
      compressibility[    2]={ 0.00000e+00,  0.00000e+00,  4.50000e-05}
   ref-p (3x3):
      ref-p[    0]={ 1.00000e+00,  0.00000e+00,  0.00000e+00}
      ref-p[    1]={ 0.00000e+00,  1.00000e+00,  0.00000e+00}
      ref-p[    2]={ 0.00000e+00,  0.00000e+00,  1.00000e+00}
   refcoord-scaling               = No
   posres-com (3):
      posres-com[0]= 0.00000e+00
      posres-com[1]= 0.00000e+00
      posres-com[2]= 0.00000e+00
   posres-comB (3):
      posres-comB[0]= 0.00000e+00
      posres-comB[1]= 0.00000e+00
      posres-comB[2]= 0.00000e+00
   QMMM                           = false
qm-opts:
   ngQM                           = 0
   constraint-algorithm           = Lincs
   continuation                   = true
   Shake-SOR                      = false
   shake-tol                      = 0.0001
   lincs-order                    = 4
   lincs-iter                     = 1
   lincs-warnangle                = 30
   nwall                          = 0
   wall-type                      = 9-3
   wall-r-linpot                  = -1
   wall-atomtype[0]               = -1
   wall-atomtype[1]               = -1
   wall-density[0]                = 0
   wall-density[1]                = 0
   wall-ewald-zfac                = 3
   pull                           = false
   awh                            = false
   rotation                       = false
   interactiveMD                  = false
   disre                          = No
   disre-weighting                = Conservative
   disre-mixed                    = false
   dr-fc                          = 1000
   dr-tau                         = 0
   nstdisreout                    = 100
   orire-fc                       = 0
   orire-tau                      = 0
   nstorireout                    = 100
   free-energy                    = no
   cos-acceleration               = 0
   deform (3x3):
      deform[    0]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      deform[    1]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
      deform[    2]={ 0.00000e+00,  0.00000e+00,  0.00000e+00}
   simulated-tempering            = false
   swapcoords                     = no
   userint1                       = 0
   userint2                       = 0
   userint3                       = 0
   userint4                       = 0
   userreal1                      = 0
   userreal2                      = 0
   userreal3                      = 0
   userreal4                      = 0
   applied-forces:
     electric-field:
       x:
         E0                       = 0
         omega                    = 0
         t0                       = 0
         sigma                    = 0
       y:
         E0                       = 0
         omega                    = 0
         t0                       = 0
         sigma                    = 0
       z:
         E0                       = 0
         omega                    = 0
         t0                       = 0
         sigma                    = 0
     density-guided-simulation:
       active                     = false
       group                      = protein
       similarity-measure         = inner-product
       atom-spreading-weight      = unity
       force-constant             = 1e+09
       gaussian-transform-spreading-width = 0.2
       gaussian-transform-spreading-range-in-multiples-of-width = 4
       reference-density-filename = reference.mrc
       nst                        = 1
       normalize-densities        = true
       adaptive-force-scaling     = false
       adaptive-force-scaling-time-constant = 4
       shift-vector               = 
       transformation-matrix      = 
grpopts:
   nrdf:     41260.8      570900
   ref-t:         312         312
   tau-t:         0.1         0.1
annealing:          No          No
annealing-npoints:           0           0
   acc:	           0           0           0
   nfreeze:           N           N           N
   energygrp-flags[  0]: 0


Reading checkpoint file md_0_10.cpt
  file generated by:     /usr/local/gromacs-2021/bin/gmx
  file generated at:     Mon Jul  1 11:44:30 2024

  GROMACS double prec.:  0
  simulation part #:     1
  step:                  40000
  time:                  80.000000

Changing nstlist from 10 to 50, rlist from 1 to 1.114


Initializing Domain Decomposition on 20 ranks
Dynamic load balancing: auto
Using update groups, nr 103496, average size 2.9 atoms, max. radius 0.139 nm
Minimum cell size due to atom displacement: 0.420 nm
Initial maximum distances in bonded interactions:
    two-body bonded interactions: 0.454 nm, LJ-14, atoms 12106 12915
  multi-body bonded interactions: 0.497 nm, CMAP Dih., atoms 1132 1145
Minimum cell size due to bonded interactions: 0.547 nm
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Guess for relative PME load: 0.19
Will use 16 particle-particle and 4 PME only ranks
This is a guess, check the performance at the end of the log file
Using 4 separate PME ranks, as guessed by mdrun
Optimizing the DD grid for 16 cells with a minimum initial size of 0.684 nm
The maximum allowed number of cells is: X 19 Y 19 Z 16
Domain decomposition grid 4 x 4 x 1, separate PME ranks 4
PME domain decomposition: 4 x 1 x 1
Interleaving PP and PME ranks
This rank does only particle-particle work.
Domain decomposition rank 0, coordinates 0 0 0

The initial number of communication pulses is: X 1 Y 1
The initial domain decomposition cell size is: X 3.34 nm Y 3.34 nm

The maximum allowed distance for atom groups involved in interactions is:
                 non-bonded interactions           1.392 nm
(the following are initial values, they could change due to box deformation)
            two-body bonded interactions  (-rdd)   1.392 nm
          multi-body bonded interactions  (-rdd)   1.392 nm

When dynamic load balancing gets turned on, these settings will change to:
The maximum number of communication pulses is: X 1 Y 1
The minimum size for domain decomposition cells is 1.392 nm
The requested allowed shrink of DD cells (option -dds) is: 0.80
The allowed shrink of domain decomposition cells is: X 0.42 Y 0.42
The maximum allowed distance for atom groups involved in interactions is:
                 non-bonded interactions           1.392 nm
            two-body bonded interactions  (-rdd)   1.392 nm
          multi-body bonded interactions  (-rdd)   1.392 nm

Using 20 MPI threads
Using 1 OpenMP thread per tMPI thread

Pinning threads with an auto-selected logical core stride of 1
System total charge: 0.000
Will do PME sum in reciprocal space for electrostatic interactions.

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen 
A smooth particle mesh Ewald method
J. Chem. Phys. 103 (1995) pp. 8577-8592
-------- -------- --- Thank You --- -------- --------

Using a Gaussian width (1/beta) of 0.320163 nm for Ewald
Potential shift: LJ r^-12: -1.000e+00 r^-6: -1.000e+00, Ewald -1.000e-05
Initialized non-bonded Ewald tables, spacing: 9.33e-04 size: 1073

Generated table with 1056 data points for 1-4 COUL.
Tabscale = 500 points/nm
Generated table with 1056 data points for 1-4 LJ6.
Tabscale = 500 points/nm
Generated table with 1056 data points for 1-4 LJ12.
Tabscale = 500 points/nm
Long Range LJ corr.: <C6> 3.1552e-04


Using SIMD 4x8 nonbonded short-range kernels

Using a dual 4x8 pair-list setup updated with dynamic pruning:
  outer list: updated every 50 steps, buffer 0.114 nm, rlist 1.114 nm
  inner list: updated every 12 steps, buffer 0.002 nm, rlist 1.002 nm
At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
  outer list: updated every 50 steps, buffer 0.244 nm, rlist 1.244 nm
  inner list: updated every 12 steps, buffer 0.048 nm, rlist 1.048 nm

Using Lorentz-Berthelot Lennard-Jones combination rule

Initializing LINear Constraint Solver

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
B. Hess and H. Bekker and H. J. C. Berendsen and J. G. E. M. Fraaije
LINCS: A Linear Constraint Solver for molecular simulations
J. Comp. Chem. 18 (1997) pp. 1463-1472
-------- -------- --- Thank You --- -------- --------

The number of constraints is 8113

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
S. Miyamoto and P. A. Kollman
SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid
Water Models
J. Comp. Chem. 13 (1992) pp. 952-962
-------- -------- --- Thank You --- -------- --------


Linking all bonded interactions to atoms


Intra-simulation communication will occur every 10 steps.

++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
G. Bussi, D. Donadio and M. Parrinello
Canonical sampling through velocity rescaling
J. Chem. Phys. 126 (2007) pp. 014101
-------- -------- --- Thank You --- -------- --------

There are: 301909 Atoms
Atom distribution over 16 domains: av 18869 stddev 209 min 18606 max 19226
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
  0:  rest

Started mdrun on rank 0 Wed Jul 24 17:29:07 2024

           Step           Time
          40000       80.00000

   Energies (kJ/mol)
           Bond            U-B    Proper Dih.  Improper Dih.      CMAP Dih.
    1.37719e+04    3.74942e+04    2.57727e+04    2.24433e+03   -6.19757e+03
          LJ-14     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)
    1.14455e+04    2.10794e+05    6.46226e+05   -3.89970e+04   -4.91123e+06
   Coul. recip.      Potential    Kinetic En.   Total Energy  Conserved En.
    2.74649e+04   -3.98121e+06    7.92987e+05   -3.18823e+06   -3.18295e+06
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
    3.11599e+02   -2.10137e+02   -3.11687e+01    4.77613e-06


DD  step 40049 load imb.: force 33.6%  pme mesh/force 0.962

step 40150 Turning on dynamic load balancing, because the performance loss due to load imbalance is 23.7 %.

DD  load balancing is limited by minimum cell size in dimension Y
DD  step 44999  vol min/aver 0.557! load imb.: force  1.6%  pme mesh/force 0.908
           Step           Time
          45000       90.00000

   Energies (kJ/mol)
           Bond            U-B    Proper Dih.  Improper Dih.      CMAP Dih.
    1.36345e+04    3.77754e+04    2.57519e+04    2.34234e+03   -6.19262e+03
          LJ-14     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)
    1.17984e+04    2.10424e+05    6.48726e+05   -3.89705e+04   -4.91216e+06
   Coul. recip.      Potential    Kinetic En.   Total Energy  Conserved En.
    2.76538e+04   -3.97922e+06    7.93404e+05   -3.18581e+06   -3.18233e+06
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
    3.11763e+02   -2.09852e+02    5.47710e+01    4.72648e-06


DD  load balancing is limited by minimum cell size in dimension Y
DD  step 49999  vol min/aver 0.558! load imb.: force  2.1%  pme mesh/force 0.944
           Step           Time
          50000      100.00000

   Energies (kJ/mol)
           Bond            U-B    Proper Dih.  Improper Dih.      CMAP Dih.
    1.34509e+04    3.80536e+04    2.57576e+04    2.40310e+03   -6.19023e+03
          LJ-14     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)
    1.15313e+04    2.10325e+05    6.46529e+05   -3.89138e+04   -4.90962e+06
   Coul. recip.      Potential    Kinetic En.   Total Energy  Conserved En.
    2.77246e+04   -3.97895e+06    7.94077e+05   -3.18488e+06   -3.18176e+06
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
    3.12027e+02   -2.09241e+02    2.89424e+00    4.79666e-06



Received the INT signal, stopping within 50 steps

           Step           Time
          53100      106.20000

Writing checkpoint, step 53100 at Wed Jul 24 17:32:58 2024


   Energies (kJ/mol)
           Bond            U-B    Proper Dih.  Improper Dih.      CMAP Dih.
    1.38074e+04    3.74218e+04    2.56170e+04    2.29479e+03   -6.13790e+03
          LJ-14     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)
    1.16823e+04    2.11045e+05    6.42031e+05   -3.89991e+04   -4.90462e+06
   Coul. recip.      Potential    Kinetic En.   Total Energy  Conserved En.
    2.76868e+04   -3.97817e+06    7.93927e+05   -3.18424e+06   -3.18137e+06
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
    3.11968e+02   -2.10159e+02   -3.68666e+01    4.84680e-06


Energy conservation over simulation part #2 of length 26.2 ns, time 80 to 106.2 ns
  Conserved energy drift: 1.99e-04 kJ/mol/ps per atom


	<======  ###############  ==>
	<====  A V E R A G E S  ====>
	<==  ###############  ======>

	Statistics over 13101 steps using 132 frames

   Energies (kJ/mol)
           Bond            U-B    Proper Dih.  Improper Dih.      CMAP Dih.
    1.37712e+04    3.77501e+04    2.57632e+04    2.31173e+03   -6.13999e+03
          LJ-14     Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)
    1.16060e+04    2.10553e+05    6.45933e+05   -3.89660e+04   -4.90912e+06
   Coul. recip.      Potential    Kinetic En.   Total Energy  Conserved En.
    2.76298e+04   -3.97891e+06    7.94051e+05   -3.18486e+06   -3.18215e+06
    Temperature Pres. DC (bar) Pressure (bar)   Constr. rmsd
    3.12017e+02   -2.09803e+02    4.63805e+00    0.00000e+00

          Box-X          Box-Y          Box-Z
    1.63452e+01    1.63452e+01    1.15578e+01

   Total Virial (kJ/mol)
    2.64296e+05    4.25187e+02    5.56541e+02
    4.24122e+02    2.64496e+05    3.60746e+02
    5.55758e+02    3.61083e+02    2.63971e+05

   Pressure (bar)
    4.28584e+00   -6.06048e+00   -6.99203e+00
   -6.04903e+00    3.24024e+00   -2.73684e+00
   -6.98360e+00   -2.74047e+00    6.38806e+00

      T-Protein  T-non-Protein
    3.12139e+02    3.12008e+02


	M E G A - F L O P S   A C C O U N T I N G

 NB=Group-cutoff nonbonded kernels    NxN=N-by-N cluster Verlet kernels
 RF=Reaction-Field  VdW=Van der Waals  QSTab=quadratic-spline table
 W3=SPC/TIP3p  W4=TIP4p (single or pairs)
 V&F=Potential and force  V=Potential only  F=Force only

 Computing:                               M-Number         M-Flops  % Flops
-----------------------------------------------------------------------------
 Pair Search distance check           37677.763752      339099.874     0.2
 NxN Ewald Elec. + LJ [F]           1268687.785616    83733393.851    51.4
 NxN Ewald Elec. + LJ [V&F]           12912.818672     1381671.598     0.8
 NxN LJ [F]                              17.421504         574.910     0.0
 NxN LJ [V&F]                             0.175168           7.532     0.0
 NxN Ewald Elec. [F]                1121559.851568    68415150.946    42.0
 NxN Ewald Elec. [V&F]                11416.073680      958950.189     0.6
 1,4 nonbonded interactions             566.971977       51027.478     0.0
 Calc Weights                         11865.929427      427173.459     0.3
 Spread Q Bspline                    253139.827776      506279.656     0.3
 Gather F Bspline                    253139.827776     1518838.967     0.9
 3D-FFT                              592459.946298     4739679.570     2.9
 Solve PME                              141.700416        9068.827     0.0
 Reset In Box                            79.100158         237.300     0.0
 CG-CoM                                  79.402067         238.206     0.0
 Bonds                                  112.105257        6614.210     0.0
 Propers                                481.160427      110185.738     0.1
 Impropers                               35.765730        7439.272     0.0
 Virial                                 396.746619        7141.439     0.0
 Stop-CM                                 39.851988         398.520     0.0
 Calc-Ekin                              791.605398       21373.346     0.0
 Lincs                                  106.288413        6377.305     0.0
 Lincs-Mat                              537.665040        2150.660     0.0
 Constraint-V                          3952.257276       35570.315     0.0
 Constraint-Vir                         384.861093        9236.666     0.0
 Settle                                1246.560150      461227.256     0.3
 CMAP                                    14.096676       23964.349     0.0
 Urey-Bradley                           393.252717       71965.247     0.0
-----------------------------------------------------------------------------
 Total                                               162845036.685   100.0
-----------------------------------------------------------------------------


    D O M A I N   D E C O M P O S I T I O N   S T A T I S T I C S

 av. #atoms communicated per step for force:  2 x 304667.7


Dynamic load balancing report:
 DLB was turned on during the run due to measured imbalance.
 Average load imbalance: 3.3%.
 The balanceable part of the MD step is 86%, load imbalance is computed from this.
 Part of the total run time spent waiting due to load imbalance: 2.8%.
 Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 1 %
 Average PME mesh/force load: 0.918
 Part of the total run time spent waiting due to PP/PME imbalance: 1.4 %


     R E A L   C Y C L E   A N D   T I M E   A C C O U N T I N G

On 16 MPI ranks doing PP, and
on 4 MPI ranks doing PME

 Computing:          Num   Num      Call    Wall time         Giga-Cycles
                     Ranks Threads  Count      (s)         total sum    %
-----------------------------------------------------------------------------
 Domain decomp.        16    1        262       2.841        164.099   1.0
 DD comm. load         16    1        262       0.048          2.795   0.0
 DD comm. bounds       16    1        260       0.097          5.631   0.0
 Send X to PME         16    1      13101       1.778        102.706   0.6
 Neighbor search       16    1        263       8.727        504.034   3.0
 Comm. coord.          16    1      12838       7.089        409.447   2.4
 Force                 16    1      13101     179.711      10379.074  62.0
 Wait + Comm. F        16    1      13101      12.829        740.945   4.4
 PME mesh *             4    1      13101     177.735       2566.228  15.3
 PME wait for PP *                             54.074        780.749   4.7
 Wait + Recv. PME F    16    1      13101       2.103        121.485   0.7
 NB X/F buffer ops.    16    1      38777       7.421        428.621   2.6
 Write traj.           16    1          4       0.073          4.222   0.0
 Update                16    1      13101       3.416        197.285   1.2
 Constraints           16    1      13101       3.059        176.642   1.1
 Comm. energies        16    1       1311       1.900        109.724   0.7
 Rest                                           0.716         41.357   0.2
-----------------------------------------------------------------------------
 Total                                        231.811      16735.084 100.0
-----------------------------------------------------------------------------
(*) Note that with separate PME ranks, the walltime column actually sums to
    twice the total reported, but the cycle count total and % are correct.
-----------------------------------------------------------------------------
 Breakdown of PME mesh computation
-----------------------------------------------------------------------------
 PME redist. X/F        4    1      26202      32.119        463.755   2.8
 PME spread             4    1      13101      62.628        904.262   5.4
 PME gather             4    1      13101      37.275        538.201   3.2
 PME 3D-FFT             4    1      26202      34.073        491.971   2.9
 PME 3D-FFT Comm.       4    1      26202       6.222         89.830   0.5
 PME solve Elec         4    1      13101       5.356         77.333   0.5
-----------------------------------------------------------------------------

               Core t (s)   Wall t (s)        (%)
       Time:     4636.222      231.811     2000.0
                 (ns/day)    (hour/ns)
Performance:        9.766        2.458
Finished mdrun on rank 0 Wed Jul 24 17:32:59 2024

